Tissue culture is a useful tool for plant scientists and horticulturalists in large part because it allows them to produce clones. Inconveniently, however, these clones are not always identical to the original, as one might expect them to be. In a report in GENETICS, Han et al. examined how propagation by tissue culture induces heritable epigenomic changes in maize.

When a portion of a plant is grown in tissue culture, it de-differentiates into an amorphous callus. This deprogrammed tissue can be induced to form roots or shoots or even to regenerate an entire plant—but this complex process can leave its marks on the genome and epigenome of the progeny. To get a picture of how tissue culture affects the epigenome, the authors compared methylation patterns in parental plants, plants that had been cultured, and the progeny of those cultured plants.

They found that most methylation was highly stable; it was consistent among all plants and unaffected by culturing. However, a subset of the methylome was variable between cultured and uncultured plants. Many of these DNA methylation differences were passed on to the progeny of the cultured plants. Importantly, some of the changes the authors identified were shared among independently regenerated progeny, suggesting that tissue culture can prompt consistent, heritable epigenetic effects in maize.

In theory, these epigenetic changes might be due to general stress; for example, the culture process might cause the methylation machinery to become dysregulated. However, since most methylation in the genome was largely unaffected, and many changes were consistent among cultured plants, it’s more likely that these changes are targeted, with certain alleles being more sensitive than others to heritable epigenetic changes during culture. The mechanisms that lead to methylation modifications and the genetic and phenotypic consequences of those changes will be interesting avenues for further study; however, since most plant genome editing requires a culture step, researchers should be cautious about unintended epigenetic consequences.